Tao Liu (τν) edited this page Feb 12, 2016 · 23 revisions

Model-based Analysis for ChIP-Seq

Quick Links:

  1. Report of MACS2 CPU and Memory Usage need update
  2. How to Install MACS2
  3. How to Build Signal Track and How to Make Simple Coverage Track
  4. How to Call Narrow Peak and Improve Resolution
  5. How to Call Broader Peak
  6. How to Deal With Pair-end Data
  7. How to Call Differential Binding events
  8. Advanced Topic: How to Call peaks using MACS2 subcommands so that you can fully customize the analysis


Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples.

Now, the stable version is version 1.4.3.

And, the stable release of MACS2 is version 2.0.10. You can check out development codes from Github


First version MACS was written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab. And Now Tao Liu is the main developer. Ben Schiller helped with differential calling module and pair-end sequencing support. Many users of MACS community contribute their patches.

Source Code



Our paper has been published in Genome Biology. Please cite "Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137".


This software is distributed under the terms of BSD License.


If you have any comments, suggestions, questions, bug reports, etc, feel free to contact: macs dot supporter at gmail. And PLEASE attach your command line and log messages if possible.

If you think your question/comment may be interesting to the MACS user group, please post it to our google group.